Custom containers

If a pipeline cannot be constructed with bioconda and therefore cannot be found on biocontainers, please contact @core-team on slack to discuss the best way to proceed. If possible, we prefer to mirror the container and host it on quay.io in the nf-core organisation to ensure future reproducibility (ie. that a container that the pipeline relies on will not be deleted by a 3rd party in the future). To do this, a core-team member should run the following commands:

docker pull <ORGANISATION>/<TOOL>:<TAG>
docker tag <ORGANISATION>/<TOOL>:<TAG> quay.io/nf-core/TOOL:<TAG>
docker push quay.io/nf-core/TOOL:<TAG>

Once this is done, please go on to the quay.io website, and check the newly updated repository’s settings (that’s the quay.io name for the container) and make sure that its visibility is public.